Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

ENA first public
2015-01-29
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2677889
INSDC center alias
Cambridge Institute - Cancer Research UK and University of Cambridge
INSDC center name
Cambridge Institute - Cancer Research UK and University of Cambridge
INSDC first public
2015-01-29T17:02:59Z
INSDC last update
2018-03-08T18:47:35Z
INSDC status
public
Submitter Id
E-MTAB-2633_rev:CRI8
broker name
ArrayExpress
common name
human
developmental stage
adult
genotype
wild type
individual
CRI8
organism part
liver
sample name
E-MTAB-2633_rev:CRI8
sex
non-identifiable human individual
specimen with known storage state
fresh specimen

Sequenced DNA Library

library_name
DVL3-11#4
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For fresh specimens, hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by cross-linking of the diced tissue in 1% formaldehyde solution for 20 minutes, addition of 250 mM glycine and incubation for a further After homogenization of cross-linked liver tissue in a dounce tissue grinder, hepatocytes were rinsed with PBS and lysed according to published protocols {Schmidt, 2009} to solubilize DNA-protein complexes. Chromatin was fragmented to 300 bp average size 1) Immunoprecipitation. Chromatin from 0.1 g of dounced liver tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339) and H3K27Ac (abcam ab4729) and automated 96-well protocols in an Agilent Bravo liquid handling rob

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
56764859
Reads aligned (%)
92.4
Duplicates removed (%)
4.1
Number of peaks
13180 (qval < 1E-05)

hg19

Number of total reads
56764859
Reads aligned (%)
91.7
Duplicates removed (%)
5.2
Number of peaks
13152 (qval < 1E-05)

Base call quality data from DBCLS SRA